Issues

• Run 2D models on 3D input

  enhancementmedium-priority
  kreshuklab/panseg#612 · Filter by author KRiedmiller opened on Sep 28, 2026
  

• Chore: Update BioImageIO Spec and Core

  kreshuklab/panseg#611 · Filter by author KRiedmiller opened on Sep 28, 2026
  

• Add run button to workflow editor

  enhancementGUIheadless
  kreshuklab/panseg#608 · Filter by author KRiedmiller opened on Sep 24, 2026
  

• BioimageIO compatibility of our models

  BioImage.IOenhancementmedium-priority
  kreshuklab/panseg#551 · Filter by author KRiedmiller opened on Mar 20, 2026
  1

  

• Model maybe too sensitive to signal variance

  question
  kreshuklab/panseg#550 · Filter by author alscunha opened on Mar 20, 2026
  2

• Better BioimageIO support

  BioImage.IObugmedium-priority
  kreshuklab/panseg#534 · Filter by author KRiedmiller opened on Feb 26, 2026
  1

• Filter pretrained models in training tab

  enhancementGUIlow-priority
  kreshuklab/panseg#517 · Filter by author KRiedmiller opened on Nov 27, 2025

• Batch Editor should mimick Napari

  GUIheadlessquestion
  kreshuklab/panseg#441 · Filter by author KRiedmiller opened on May 23, 2025
  

• Handle invalid tasks for workflows

  enhancementlow-priority
  kreshuklab/panseg#430 · Filter by author KRiedmiller opened on May 12, 2025
  

• Example config.yaml for current plant-seg version missing

  headless
  kreshuklab/panseg#340 · Filter by author Dampfnudeldroid opened on Oct 1, 2024
  1

• Model resolution should allow None to avoid a default like (1.0, 1.0, 1.0)

  bug
  kreshuklab/panseg#254 · Filter by author qin-yu opened on May 29, 2024
  2

  

• Need to make use of predictions from multiple models

  enhancementGUI
  kreshuklab/panseg#225 · Filter by author qin-yu opened on Apr 25, 2024
  

• Re-train all PlantSeg models to eliminate hallucination during inference

  BioImage.IObugenhancementmedium-priority
  kreshuklab/panseg#224 · Filter by author qin-yu opened on Apr 17, 2024
  2

  

• It would be nice to know exactly which instances are removed by postprocessing steps

  enhancement
  kreshuklab/panseg#200 · Filter by author qin-yu opened on Feb 20, 2024

• Help to choose the correct scale to apply the network

  documentationenhancementGUI
  kreshuklab/panseg#189 · Filter by author Buglakova opened on Feb 5, 2024
  2

  

• Erosion option for nuclei channel in Lifted MultiCut and Segmentation Fix in Extra-Seg

  enhancement
  kreshuklab/panseg#186 · Filter by author qin-yu opened on Jan 31, 2024